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Masters Degrees (Medical Microbiology)

Permanent URI for this collectionhttps://hdl.handle.net/10413/9620

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Browsing Masters Degrees (Medical Microbiology) by Subject "Antimicrobial resistance."

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    Induction of secondary metabolite production in endophytic fungi isolated from Albizia adianthifolia using multiple small compounds involved in fungal chromatin remodeling.
    (2021) Nekati, Lucpah Patience.; Mhlongo, Sizwe Innocent.
    Fungi are an inexhaustible source of unexplored bioactive secondary metabolites that have been useful to humans as pharmaceuticals and other valuable products. The unexplored arsenal of secondary metabolites from fungi and the growing problem of antibiotic resistance have led to the search for novel bioactive secondary metabolites in fungi from unique niches. Endophytic fungi are an unexplored niche of fungi that have a special mutualistic relationship with their hosts. Endophytic fungi and medicinal plants' relationship has received attention as endophytic fungi have been shown to produce bioactive secondary metabolites with a profile similar to secondary metabolites from their host medicinal plants. Despite the potential of endophytic fungi as an arsenal for novel pharmacological important secondary metabolites, they remain hugely unexplored due to the cryptic or silenced nature of some biosynthetic gene clusters coding for secondary metabolites. The genes that code for secondary metabolites are arranged in clusters known as biosynthetic gene clusters. Some of these biosynthetic gene clusters are sequestered away from transcription factors; thus, they are not transcribed under standard laboratory conditions. Small-molecule modifiers have been recognized as an important way of activating these silenced genes through epigenetic regulation of the chromatin. Thus, the present study sought to induce secondary metabolite production in nine endophytic fungi isolated from Albizia adianthifolia using multiple small compounds (valproic acid, quercetin, sodium butyrate, and trimethoprim) involved in fungal chromatin remodeling. The secondary metabolites were assayed for their antibacterial activity against Staphylococcus aureus, Escherichia coli, Mycobacterium smegmatis, Enterococcus faecalis, and Klebsiella pneumoniae. Antibacterial activity was observed from two untreated and quercetin and trimethoprim-treated endophytic fungi identified through nucleotide sequencing of the internal transcribed spacer of ribosomal DNA as Alternaria sp against S. aureus, E. faecalis, and M. smegmatis. Significant antibacterial activity was observed for quercetin and trimethoprim23 treated Alternaria alternata and Alternata brassicicola. However, the valproic acid-treated A. alternata showed slight antibacterial activity against the S. aureus, E. faecalis, and M. smegmatis, while no antibacterial activity was observed for valproic acid-treated A. brassicicola. No antibacterial activity was observed with sodium butyrate-treated A. alternata and A. brassicicola. The findings of this study add to the pool of studies aimed at discovering new drugs from endophytic fungi to address antimicrobial resistance. Future studies on high performance liquid chromatography to identify the active secondary metabolites from A. brassicicola and A. alternata will be done. Also, future studies to fully assess the mechanisms of chromatin remodeling in the active endophytic fungi will assist in identifying small molecule modifiers that can activate secondary metabolite production in endophytic fungi.
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    Microbial profile and antimicrobial susceptibility patterns of neonatal blood stream infections in Durban, South Africa.
    (2020) Pillay, Dharshni.; Mahabeer, Yesholata.
    Objectives Antimicrobial resistance (AMR) has emerged as a global threat to healthcare resulting in an increase in morbidity and mortality. Neonatal sepsis is ranked as the third highest cause of neonatal demise globally, in which AMR accounted for 31.0% of deaths. This study analysed the aetiology and antimicrobial resistance patterns of bloodstream infections within the neonatal intensive care unit (NICU) at a tertiary hospital in Durban, South Africa. Methods A retrospective data review was conducted on all positive blood cultures at three time periods: 2014, 2016 and 2018. The organisms and antimicrobial susceptibilities were analysed for significant trends using Poisson and logistic regression. Results A preponderance of gram-positive organisms (68.7%) over gram-negatives (26.8%) and fungi (4.5%) was detected. Common pathogens included coagulase-negative staphylococci (53.5%), Klebsiella pneumoniae (11.6%), enterococci (9.3%), and Acinetobacter baumannii (7.7%). Late-onset sepsis (86.8%) predominated over early-onset sepsis (13.2%). High rates of resistance to first- and second-line antibiotics were noted among gram-positive and gramnegative organisms. Multidrug resistant organisms included extended-spectrum betalactamase (ESBL) K. pneumoniae (7.6%) and multi-drug resistant A. baumannii (7.0%). A statistically significant decrease in ESBL-producing organisms was documented between 2014 and 2018 (p = 0.005). Conclusion High resistance rates were seen for first- and second-line antibiotics used for the treatment of neonatal sepsis. Ongoing microbial surveillance is essential to tailor empiric antimicrobial choices in individual units.
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    Molecular epidemiology of antibiotic resistant Campylobacter spp. from farm-to-fork in an intensive pig production system in Kwazulu-Natal, South Africa.
    (2021) Sithole, Viwe.; Amoako, Daniel Gyamfi.; Essack, Sabiha Yusuf.; Abia, Akebe Luther King.; Bester, Linda Antionette.
    Background: Campylobacter spp. are among the leading foodborne pathogens, causing Campylobacteriosis, a zoonotic infection that results in bacterial gastroenteritis and diarrhea disease in animals and humans. The emergence and transmission of antibiotic resistance and virulence in Campylobacter spp. is increasingly reported. We investigated the molecular epidemiology of antibiotic resistant Campylobacter spp. isolated across the farm-to-fork-continuum in an intensive pig production system in the uMgungundlovu District, Kwazulu-Natal, South Africa. Methodology: Following ethical approval, samples were collected over a period of sixteen weeks from selected critical points (farm, transport, abattoir and retail) using a farm-to-fork sampling approach according to WHO-AGISAR guidelines. Overall, 520 samples were investigated for the presence of Campylobacter spp. which were putatively identified using selective media with identity and speciation confirmed by polymerase chain reaction (PCR) of specific genes. Resistance profiles were ascertained by the Kirby-Bauer disk diffusion method according to EUCAST and/or CLSI guidelines. Selected antibiotic resistance and virulence genes were identified using PCR and DNA sequencing. Clonal relatedness among the isolates was determined using enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR). Results: Altogether, 378/520 (72.7%) samples were positive for Campylobacter spp. with C. coli as the most predominant (73.3%), followed by C. jejuni (17.7%) with 9.0% classified as “other”. Relatively high levels of resistance were observed in C. coli and C. jejuni to erythromycin (89% and 99%), streptomycin (87% and 93%), tetracycline (82% and 96%), ampicillin (69% and 85%), and ciprofloxacin (53% and 67%) respectively. The lowest percentage resistance observed was for gentamicin (12%) for both C. coli and C. jejuni, and nalidixic acid (28% and 27%) for C. coli and C. jejuni respectively. Multi-drug resistance (MDR) was noted among 330/378 (87.3%) isolates. The antibiotic resistance genes observed were the tetO (74.6%), the blaOXA-61 (2.9%) and cmeB (11.1%) accounting for the resistance to tetracycline and ampicillin while the membrane efflux pump could confer resistance to ampicillin, tetracycline, ciprofloxacin, and erythromycin. All C. coli and C. jejuni isolates (21) with the gyrA gene exhibited mutation at the Thr-86-Ile region in the quinolone-resistancedetermining region (QRDR) and all C. coli and C. jejuni isolates (18) exhibiting erythromycin resistance showed common transitional mutations A2075G and A2074C in the 23S rRNA gene. Of the virulence genes tested, ciaB, dnaJ, pldA, cdtA, cdtB, cdtC and cadF were detected in 48.6%, 61.1 %, 17.4%, 67.4%, 19.3%, 51% and 5% of all Campylobacter isolates respectively. The ERIC-PCR banding patterns revealed that isolates along the continuum were highly diverse with isolates from the same sampling points belonging to the same major ERIC-types. Conclusion: We showed relatively high levels of resistance to antibiotics commonly used in intensive pig production in South Africa with some evidence, albeit minimal, of transmission across the farm-tofork continuum. This together with the virulence profiles present in Campylobacter spp. presents a challenge to food safety and a potential risk to human health. This is further exacerbated by the reduction in antibiotic treatment options necessitating routine surveillance and monitoring together with antibiotic stewardship, comprehensive biosecurity, and good animal husbandry in intensive pig production.